rs1511024

chr4-119319026-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000134.4(FABP2):c.*15G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 1,585,764 control chromosomes in the GnomAD database, including 1,113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.041 (193 hom., cov: 32)
  • Exomes 𝑓: 0.033 (920 hom.)
• Consequence: FABP2 NM_000134.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.286

Genes affected

FABP2 (HGNC:3556): (fatty acid binding protein 2) The protein encoded by this gene is an intracellular fatty acid-binding protein that participates in the uptake, intracellular metabolism, and transport of long-chain fatty acids. The encoded protein is also involved in the modulation of cell growth and proliferation. This protein binds saturated long-chain fatty acids with high affinity, and may act as a lipid sensor to maintain energy homeostasis. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 4-119319026-C-T is Benign according to our data. Variant chr4-119319026-C-T is described in ClinVar as [Benign]. Clinvar id is 1226479.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP2	NM_000134.4	c.*15G>A		3_prime_UTR_variant	4/4	ENST00000274024.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP2	ENST00000274024.4	c.*15G>A		3_prime_UTR_variant	4/4	1	NM_000134.4	P1

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6292 AN: 151858 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.0321

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0418

GnomAD3 exomes AF: 0.0325 AC: 7602 AN: 234116 Hom.: 184 AF XY: 0.0330 AC XY: 4207 AN XY: 127550

Gnomad AFR exome AF: 0.0629

Gnomad AMR exome AF: 0.0185

Gnomad ASJ exome AF: 0.0164

Gnomad EAS exome AF: 0.00569

Gnomad SAS exome AF: 0.0373

Gnomad FIN exome AF: 0.0377

Gnomad NFE exome AF: 0.0352

Gnomad OTH exome AF: 0.0385

GnomAD4 exome AF: 0.0329 AC: 47174 AN: 1433788 Hom.: 920 Cov.: 28 AF XY: 0.0330 AC XY: 23580 AN XY: 714010

Gnomad4 AFR exome AF: 0.0584

Gnomad4 AMR exome AF: 0.0212

Gnomad4 ASJ exome AF: 0.0168

Gnomad4 EAS exome AF: 0.0147

Gnomad4 SAS exome AF: 0.0372

Gnomad4 FIN exome AF: 0.0388

Gnomad4 NFE exome AF: 0.0325

Gnomad4 OTH exome AF: 0.0349

GnomAD4 genome AF: 0.0415 AC: 6301 AN: 151976 Hom.: 193 Cov.: 32 AF XY: 0.0418 AC XY: 3106 AN XY: 74292

Gnomad4 AFR AF: 0.0641

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.00580

Gnomad4 SAS AF: 0.0322

Gnomad4 FIN AF: 0.0373

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0447

Alfa AF: 0.0347 Hom.: 39

Bravo AF: 0.0411

Asia WGS AF: 0.0360 AC: 124 AN: 3458

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.1
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1511024; hg19: chr4-120240181;